Gary Brawer at Stringed Instrument Repair does good work. He's worked on Satriani and Schon's guitars. Another guy is Charles Duck, he closed his shop a year ago, but if you can find him he does good work too.
For amplifiers, go with Dan Torres (Torres Engineering) in San Mateo. I've ben going to him for little tweaks every now and then. He's one informed dude! He also knows his way around guitar electronics and pups too.